Merge branch 'refactor' of https://github.com/josephmje/dmriprep into refactor

Author: josephmje

.flake8

@@ -8,9 +8,6 @@ Development Leads
 - Anisha Keshavan <[email protected]> [Corresponding developer]
 - Adam Richie-Halford <[email protected]>
 
-- Michael Joseph <[email protected]> [Corresponding developer]
-- Salim Mansour <[email protected]>
-
 Contributors
 ------------
 

.pre-commit-config.yaml

@@ -1,27 +1,35 @@
 # Use Ubuntu 16.04 LTS
 FROM ubuntu:xenial-20190610
 
-# Used command:
-# neurodocker generate docker --base=debian:stretch --pkg-manager=apt
-# --ants version=latest method=source --mrtrix3 version=3.0_RC3
-# --freesurfer version=6.0.0 method=binaries --fsl version=6.0.1 method=binaries
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    xvfb \
+                    cython3 \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config \
+                    git && \
+    curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
+    apt-get install -y --no-install-recommends \
+                    nodejs && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Getting required installation tools
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
         apt-utils \
-        bzip2 \
-        ca-certificates \
-        curl \
         locales \
         unzip \
         bc \
-        libtool \
         tar \
         dpkg \
         wget \
         gcc \
-        git \
         libstdc++6
 
 # Neurodocker Setup
@@ -56,27 +64,21 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
 
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
-# install ANTS v2.3.1
-curl -sSL https://github.com/ANTsX/ANTs/archive/v2.3.1.tar.gz
-
+# Installing ANTS v2.3.1
+ENV ANTSPATH=/opt/ants
+RUN mkdir -p $ANTSPATH && \
+    curl -sSL https://github.com/ANTsX/ANTs/archive/v2.3.1.tar.gz
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=$ANTSPATH:$PATH
 
-# ANTS (used from BIDS-Apps https://github.com/BIDS-Apps/dockerfile-templates/blob/master/ANTs/Dockerfile)
-RUN mkdir -p /opt/ants && \
-    curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
-    | tar -xjC /opt/ants --strip-components 1 && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-ENV ANTSPATH /opt/ants
-ENV PATH $ANTSPATH:$PATH
-
-# MRtrix3 generated from Neurodocker
+# Installing MRtrix3
 ENV PATH="/opt/mrtrix3-3.0_RC3/bin:$PATH"
 RUN echo "Downloading MRtrix3 ..." \
     && mkdir -p /opt/mrtrix3-3.0_RC3 \
     && curl -fsSL --retry 5 https://dl.dropbox.com/s/2oh339ehcxcf8xf/mrtrix3-3.0_RC3-Linux-centos6.9-x86_64.tar.gz \
     | tar -xz -C /opt/mrtrix3-3.0_RC3 --strip-components 1
 
-# Freesurfer generated from Neurodocker
+# Installing Freesurfer
 ENV FREESURFER_HOME="/opt/freesurfer-6.0.0" \
     PATH="/opt/freesurfer-6.0.0/bin:$PATH"
 RUN apt-get update -qq \
@@ -108,6 +110,7 @@ RUN apt-get update -qq \
          --exclude='freesurfer/trctrain' \
     && sed -i '$isource "/opt/freesurfer-6.0.0/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
 
+# Installing FSL
 ENV FSLDIR="/opt/fsl-6.0.1" \
     PATH="/opt/fsl-6.0.1/bin:$PATH"
 RUN apt-get update -qq \
@@ -183,15 +186,6 @@ RUN echo '{ \
     \n  ] \
     \n}' > /neurodocker/neurodocker_specs.json
 
-#All of the examples below use debian:stretch as the base image, but any Docker image can be used as a base.
-#Common base images (and their packages managers) are ubuntu:16.04 (apt), centos:7 (yum), neurodebian:nd16.04 (apt), and neurodebian:stretch (apt).
-
-# FSL 6.0.1
-# Freesurfer 6.0.0
-# MRtrix3
-# ANTS
-# Python 3
-
 # add credentials on build
 RUN mkdir ~/.ssh && ln -s /run/secrets/host_ssh_key ~/.ssh/id_rsa
 # Getting required installation tools

AUTHORS.rst

@@ -1,18 +1,18 @@
-.. highlight:: shell
-
-===========
+========
 dmriprep
-===========
-
-.. image:: https://codecov.io/gh/TIGRLab/dmriprep/branch/master/graph/badge.svg
-  :alt: Codecov Badge
-  :target: https://codecov.io/gh/TIGRLab/dmriprep
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
-  :alt: Black Badge
-  :target: https://github.com/python/black
-.. image:: https://api.codacy.com/project/badge/Grade/f45ec5c64894427a8860cc87cda1910a
-   :alt: Codacy Badge
-   :target: https://app.codacy.com/app/josephmje/dmriprep?utm_source=github.com&utm_medium=referral&utm_content=TIGRLab/dmriprep&utm_campaign=Badge_Grade_Dashboard
+========
+
+
+.. image:: https://img.shields.io/pypi/v/dmriprep.svg
+        :target: https://pypi.python.org/pypi/dmriprep
+
+.. image:: https://img.shields.io/travis/akeshavan/dmriprep.svg
+        :target: https://travis-ci.org/akeshavan/dmriprep
+
+.. image:: https://readthedocs.org/projects/dmriprep/badge/?version=latest
+        :target: https://dmriprep.readthedocs.io/en/latest/?badge=latest
+        :alt: Documentation Status
+
 
 Preprocessing of neuroimaging data in preparation for AFQ analysis
 ------------------------------------------------------------------

Dockerfile

@@ -196,7 +196,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     if verbose:
         print("likely tags: %s" % ",".join(sorted(tags)))
     for ref in sorted(tags):
-        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        # sorting will prefer e.g., "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
             if verbose:
@@ -483,6 +483,20 @@ def get_versions():
 
     cfg = get_config()
     verbose = cfg.verbose
+    root = os.path.realpath(__file__)
+
+    root_dir = os.path.dirname(root)
+    if os.path.isfile(os.path.join(root_dir, 'VERSION')):
+        with open(os.path.join(root_dir, 'VERSION')) as vfile:
+            version = vfile.readline().strip()
+
+        return {
+            "version": version,
+            "full-revisionid": None,
+            "dirty": None,
+            "error": None,
+            "date": None
+        }
 
     try:
         return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
@@ -491,7 +505,6 @@ def get_versions():
         pass
 
     try:
-        root = os.path.realpath(__file__)
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.

README.rst

@@ -23,30 +23,29 @@ def __init__(
         layout,
         subject_list,
         bids_dir,
-        work_dir,
         output_dir,
-        # concat_shells,
+        analysis_level,
+        work_dir,
+        ignore,
         b0_thresh,
-        resize_scale,
-        omp_nthreads,
-        eddy_niter,
+        output_resolution,
         bet_dwi,
         bet_mag,
-        ignore,
-        analysis_level,
+        omp_nthreads,
+        eddy_niter,
         synb0_dir,
-        acqp_file,
+        acqp_file
     ):
+
+        self.layout = layout
+        self.subject_list = subject_list
         self.bids_dir = bids_dir
         self.output_dir = output_dir
         self.analysis_level = analysis_level
-        self.layout = layout
-        self.subject_list = subject_list
         self.work_dir = work_dir
-        # self.concat_shells = concat_shells
         self.ignore = ignore
-        self.resize_scale = resize_scale
         self.b0_thresh = b0_thresh
+        self.output_resolution = resize_scale
         self.bet_dwi = bet_dwi
         self.bet_mag = bet_mag
         self.omp_nthreads = omp_nthreads
@@ -95,7 +94,9 @@ def __init__(
     type=click.IntRange(min=0, max=10),
 )
 @click.option(
-    "--resize_scale", help="Scale factor to resize DWI image", type=float
+    "--output_resolution",
+    help="The isotropic voxel size in mm the data will be resampled to before eddy.",
+    type=float
 )
 # specific options for eddy
 @click.option(
@@ -153,6 +154,18 @@ def __init__(
     help="working directory",
     type=click.Path(exists=True, file_okay=False, writable=True),
 )
+@click.option(
+    "--tbss",
+    help="Run TBSS"
+    is_flag=True
+)
+@click.option(
+    "--diffusivity_meas",
+    help="Specify which measures to calculate.",
+    default=("FA",),
+    type=click.Choice(["FA", "MD", "AD", "RD"]),
+    multiple=True
+)
 @click.option(
     "--synb0_dir",
     default=None,
@@ -163,17 +176,16 @@ def main(
     participant_label,
     bids_dir,
     output_dir,
-    work_dir,
-    skip_bids_validation,
     analysis_level,
+    skip_bids_validation,
+    work_dir,
+    ignore,
     b0_thresh,
-    # concat_shells,
-    resize_scale,
-    omp_nthreads,
-    eddy_niter,
+    output_resolution,
     bet_dwi,
     bet_mag,
-    ignore,
+    omp_nthreads,
+    eddy_niter,
     synb0_dir,
     acqp_file,
 ):
@@ -195,7 +207,7 @@ def main(
             "is participant at the moment."
         )
 
-    layout = BIDSLayout(bids_dir, validate=False)
+    layout = BIDSLayout(bids_dir, validate=True)
     all_subjects, subject_list = collect_participants(
         layout, participant_label=participant_label
     )
@@ -213,17 +225,16 @@ def main(
         layout=layout,
         subject_list=subject_list,
         bids_dir=bids_dir,
-        work_dir=work_dir,
         output_dir=output_dir,
-        # concat_shells=concat_shells,
+        analysis_level=analysis_level,
+        work_dir=work_dir,
+        ignore=list(ignore),
         b0_thresh=b0_thresh,
-        resize_scale=resize_scale,
-        omp_nthreads=omp_nthreads,
-        eddy_niter=eddy_niter,
+        output_resolution=output_resolution,
         bet_dwi=bet_dwi,
         bet_mag=bet_mag,
-        ignore=list(ignore),
-        analysis_level=analysis_level,
+        omp_nthreads=omp_nthreads,
+        eddy_niter=eddy_niter,
         synb0_dir=synb0_dir,
         acqp_file=acqp_file,
     )

dmriprep/_version.py

@@ -19,7 +19,7 @@ class MRResizeInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc="input DWI image",
     )
-    size = traits.List(
+    image_size = traits.List(
         traits.Int(),
         argstr="-size %s",
         desc="define the new image size for the output image. This should be "
@@ -33,7 +33,7 @@ class MRResizeInputSpec(MRTrix3BaseInputSpec):
         "dimensions, or as a comma-separated list of the size for each "
         "voxel dimension.",
     )
-    scale = traits.Float(
+    scale_factor = traits.Float(
         argstr="-scale %s",
         desc="scale the image resolution by the supplied factor. This can be "
         "specified either as a single value to be used for all "
@@ -75,10 +75,10 @@ class MRResize(MRTrix3Base):
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> resize = mrt.MRResize()
     >>> resize.inputs.in_file = 'dwi.mif'
-    >>> denoise.inputs.mask = 'mask.mif'
-    >>> denoise.cmdline                               # doctest: +ELLIPSIS
-    'dwidenoise -mask mask.mif dwi.mif dwi_denoised.mif'
-    >>> denoise.run()                                 # doctest: +SKIP
+    >>> resize.inputs.scal_factor = 2
+    >>> resize.cmdline                               # doctest: +ELLIPSIS
+    'mrresize -scale 2 dwi.mif dwi_resized.mif'
+    >>> resize.run()                                 # doctest: +SKIP
     """
 
     _cmd = "mrresize"

dmriprep/cli.py

@@ -54,7 +54,7 @@ def init_single_subject_wf(subject_id, name, parameters):
         if "session" in entities:
             session_id = entities["session"]
         else:
-            session_id = ""
+            session_id = None
         metadata = parameters.layout.get_metadata(dwi_file)
         dwi_preproc_wf = init_dwi_preproc_wf(
             subject_id=subject_id,
@@ -86,7 +86,10 @@ def init_single_subject_wf(subject_id, name, parameters):
         ds_inputspec.inputs.output_folder = parameters.output_dir
         ds_inputspec.inputs.metadata = metadata
 
-        wf_name = "sub_" + subject_id + "_ses_" + session_id + "_preproc_wf"
+        if session_id:
+            wf_name = "sub_" + subject_id + "_ses_" + session_id + "_preproc_wf"
+        else:
+            wf_name = "sub_" + subject_id + "_preproc_wf"
         full_wf = pe.Workflow(name=wf_name)
 
         full_wf.connect(

dmriprep/interfaces/mrtrix3.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 from .base import init_dwi_preproc_wf
-from .denoise import init_denoise_wf
-from .unring import init_unring_wf
+from .remove_artefacts import init_remove_artefacts_wf
 from .tensor import init_tensor_wf
 from .outputs import init_output_wf